[gmx-users] Dihedral not counted?
Andrea Muntean
andreamuntean at gmail.com
Mon Oct 27 17:00:20 CET 2008
Sorry,
once again for everybody in the list:
Here are the .rtp entries:
[PS1]
[atoms]
CH3 CH3 0 0
CH CH1 0 0
CB C 0 0
CG1 CR1 0 0
CG2 CR1 0 0
CG3 CR1 0 0
CG4 CR1 0 0
CG5 CR1 0 0
[bonds]
CH3 CH gb_26
CH CB gb_26
CB CG1 gb_15
CG1 CG2 gb_15
CG2 CG3 gb_15
CG3 CG4 gb_15
CG4 CG5 gb_15
CG5 CB gb_15
CH +CH2 gb_26
[angles]
;109,5 angle
CH3 CH +CH2 ga_12
CH3 CH CB ga_12
CB CH +CH2 ga_12
;120 angle
CH CB CG1 ga_26
CH CB CG5 ga_26
CG1 CB CG5 ga_26
CB CG1 CG2 ga_26
CG1 CG2 CG3 ga_26
CG2 CG3 CG4 ga_26
CG3 CG4 CG5 ga_26
CG4 CG5 CB ga_26
[impropers]
;keep the planarity of the ring
CB CG1 CG2 CG3 gi_1
CG1 CG2 CG3 CG4 gi_1
CG2 CG3 CG4 CG5 gi_1
CG3 CG4 CG5 CB gi_1
CG4 CG5 CB CG1 gi_1
CG5 CB CG1 CG2 gi_1
;around CB
CB CG1 CG5 CH gi_1
CB CG5 CH CG1 gi_1
CB CH CG1 CG5 gi_1
;around CH
CH CB +CH2 CH3 gi_1
CH +CH2 CH3 CB gi_1
CH CH3 CB +CH2 gi_1
[dihedrals]
;in the chain - 3-fold (n=3)
CH3 CH +CH2 +CH gd_16
CB CH +CH2 +CH gd_16
;around CH-CB - 2-fold (n=2)
CH3 CH CB CG5 gd_1
CH3 CH CB CG1 gd_1
+CH2 CH CB CG5 gd_1
+CH2 CH CB CG1 gd_1
;around CB-CG - 2-fold?,do we need them?
CH CB CG1 CG2
CH CB CG5 CG4
[PS]
[atoms]
CH2 CH2 0 0
CH CH1 0 0
CB C 0 0
CG1 CR1 0 0
CG2 CR1 0 0
CG3 CR1 0 0
CG4 CR1 0 0
CG5 CR1 0 0
[bonds]
-CH CH2 gb_26
CH2 CH gb_26
CH CB gb_26
CB CG1 gb_15
CG1 CG2 gb_15
CG2 CG3 gb_15
CG3 CG4 gb_15
CG4 CG5 gb_15
CG5 CB gb_15
CH +CH2 gb_26
[angles]
;109,5 angle
-CH CH2 CH ga_12
CH2 CH +CH2 ga_12
CH2 CH CB ga_12
CB CH +CH2 ga_12
;120 angle
CH CB CG1 ga_26
CH CB CG5 ga_26
CG1 CB CG5 ga_26
CB CG1 CG2 ga_26
CG1 CG2 CG3 ga_26
CG2 CG3 CG4 ga_26
CG3 CG4 CG5 ga_26
CG4 CG5 CB ga_26
[impropers]
;keep the planarity of the ring
CB CG1 CG2 CG3 gi_1
CG1 CG2 CG3 CG4 gi_1
CG2 CG3 CG4 CG5 gi_1
CG3 CG4 CG5 CB gi_1
CG4 CG5 CB CG1 gi_1
CG5 CB CG1 CG2 gi_1
;around CB
CB CG1 CG5 CH gi_1
CB CG5 CH CG1 gi_1
CB CH CG1 CG5 gi_1
;around CH
CH CB +CH2 CH2 gi_1
CH +CH2 CH2 CB gi_1
CH CH2 CB +CH2 gi_1
[dihedrals]
;in the chain - 3-fold
CH2 CH +CH2 +CH gd_16
CB CH +CH2 +CH gd_16
-CH CH2 CH CB gd_16
-CH CH2 CH +CH2 gd_16
;around CH-CB - 2-fold
CH2 CH CB CG5 gd_1
CH2 CH CB CG1 gd_1
+CH2 CH CB CG5 gd_1
+CH2 CH CB CG1 gd_1
;around CB-CG - 2-fold?,do we need them?
CH CB CG1 CG2
CH CB CG5 CG4
[ PSN ]
[atoms]
CH2 CH2 0 0
CH CH1 0 0
CB C 0 0
CG1 CR1 0 0
CG2 CR1 0 0
CG3 CR1 0 0
CG4 CR1 0 0
CG5 CR1 0 0
CH3 CH3 0 0
[bonds]
-CH CH2 gb_26
CH2 CH gb_26
CH CB gb_26
CB CG1 gb_15
CG1 CG2 gb_15
CG2 CG3 gb_15
CG3 CG4 gb_15
CG4 CG5 gb_15
CG5 CB gb_15
CH CH3 gb_26
[angles]
-CH CH2 CH ga_12
CH2 CH CH3 ga_12
CH2 CH CB ga_12
CB CH CH3 ga_12
CH CB CG1 ga_26
CH CB CG5 ga_26
CG1 CB CG5 ga_26
CB CG1 CG2 ga_26
CG1 CG2 CG3 ga_26
CG2 CG3 CG4 ga_26
CG3 CG4 CG5 ga_26
CG4 CG5 CB ga_26
[impropers]
;keep the planarity of the ring
CB CG1 CG2 CG3 gi_1
CG1 CG2 CG3 CG4 gi_1
CG2 CG3 CG4 CG5 gi_1
CG3 CG4 CG5 CB gi_1
CG4 CG5 CB CG1 gi_1
CG5 CB CG1 CG2 gi_1
;around CB
CB CG1 CG5 CH gi_1
CB CG5 CH CG1 gi_1
CB CH CG1 CG5 gi_1
;around CH
CH CB CH3 CH2 gi_1
CH CH3 CH2 CB gi_1
CH CH2 CB CH3 gi_1
[dihedrals]
;in the chain - 3-fold (n=3)
-CH CH2 CH CB gd_16
-CH CH2 CH CH3 gd_16
;around CH-CB - 2-fold (n=2)
CH2 CH CB CG5 gd_1
CH2 CH CB CG1 gd_1
CH3 CH CB CG5 gd_1
CH3 CH CB CG1 gd_1
;around CB-CG - 2-fold?,do we need them?
CH CB CG1 CG2
CH CB CG5 CG4
CB CG1 CG5 CH gi_1
CB CG5 CH CG1 gi_1
CB CH CG1 CG5 gi_1
;around CH
CH CB CH3 CH2 gi_1
CH CH3 CH2 CB gi_1
CH CH2 CB CH3 gi_1
[dihedrals]
;in the chain - 3-fold (n=3)
-CH CH2 CH CB gd_16
-CH CH2 CH CH3 gd_16
;around CH-CB - 2-fold (n=2)
CH2 CH CB CG5 gd_1
CH2 CH CB CG1 gd_1
CH3 CH CB CG5 gd_1
CH3 CH CB CG1 gd_1
;around CB-CG - 2-fold?,do we need them?
CH CB CG1 CG2
CH CB CG5 CG4
And the .top file for the trimer, only the [atoms] and [dihedrals]
(only the proper dihedrals) part:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 CH3 1 PS1 CH3 1 0 15.035 ; qtot 0
2 CH1 1 PS1 CH 1 0 13.019 ; qtot 0
3 C 1 PS1 CB 1 0 12.011 ; qtot 0
4 CR1 1 PS1 CG1 1 0 13.019 ; qtot 0
5 CR1 1 PS1 CG2 1 0 13.019 ; qtot 0
6 CR1 1 PS1 CG3 1 0 13.019 ; qtot 0
7 CR1 1 PS1 CG4 1 0 13.019 ; qtot 0
8 CR1 1 PS1 CG5 1 0 13.019 ; qtot 0
9 CH2 2 PS CH2 2 0 14.027 ; qtot 0
10 CH1 2 PS CH 2 0 13.019 ; qtot 0
11 C 2 PS CB 2 0 12.011 ; qtot 0
12 CR1 2 PS CG1 2 0 13.019 ; qtot 0
13 CR1 2 PS CG2 2 0 13.019 ; qtot 0
14 CR1 2 PS CG3 2 0 13.019 ; qtot 0
15 CR1 2 PS CG4 2 0 13.019 ; qtot 0
16 CR1 2 PS CG5 2 0 13.019 ; qtot 0
17 CH2 3 PSN CH2 3 0 14.027 ; qtot 0
18 CH1 3 PSN CH 3 0 13.019 ; qtot 0
19 C 3 PSN CB 3 0 12.011 ; qtot 0
20 CR1 3 PSN CG1 3 0 13.019 ; qtot 0
21 CR1 3 PSN CG2 3 0 13.019 ; qtot 0
22 CR1 3 PSN CG3 3 0 13.019 ; qtot 0
23 CR1 3 PSN CG4 3 0 13.019 ; qtot 0
24 CR1 3 PSN CG5 3 0 13.019 ; qtot 0
25 CH3 3 PSN CH3 3 0 15.035 ; qtot 0
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
1 2 3 4 1 gd_1
1 2 3 8 1 gd_1
9 2 3 4 1 gd_1
9 2 3 8 1 gd_1
1 2 9 10 1 gd_16
3 2 9 10 1 gd_16
2 3 4 5 1
2 3 8 7 1
2 9 10 11 1 gd_16
9 10 11 12 1 gd_1
9 10 11 16 1 gd_1
17 10 11 12 1 gd_1
17 10 11 16 1 gd_1
9 10 17 18 1 gd_16
11 10 17 18 1 gd_16
10 11 12 13 1
10 11 16 15 1
10 17 18 19 1 gd_16
10 17 18 25 1 gd_16
17 18 19 20 1 gd_1
17 18 19 24 1 gd_1
25 18 19 20 1 gd_1
25 18 19 24 1 gd_1
18 19 20 21 1
18 19 24 23 1
Cheers,
Andrea
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